Spike mutation tracker

Directory
Sequence analysis »
Visualization »

Table of Contents

1. About The Project
2. Getting Started
   • Prerequisites
   • Installation
3. Sequence analysis
4. visualization

About The Project

This repository contains scripts used to analyze and visualize mutations in the SARS-CoV-2 spike gene.

Current efforts involve detection of evolutionarily convergent SARS-CoV-2 spike mutations, mutations that enable mAb and antiviral resistance, and mutations that increase transmissibility of the disease.

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Getting Started

Scripts are compatable with Python 3.7 - Python 3.11, Pandas 1.5.1+, Biopython 1.79+, Streamlit 1.18.0+.

• Anaconda distribution package recommended for conda installations.
• Pip installation requires pip 19.3+.

Prerequisites

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Installation

Pandas

conda install pandas

pip install pandas

Biopython

conda install -c conda-forge biopython

pip install biopython

Streamlit

conda install -c conda-forge streamlit

pip install streamlit

Plotly

conda install -c plotly plotly_express

pip install plotly_express

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Sequence Analysis

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Visualization

Data visualization was performed on the sequence analysis output for SARS-CoV-2 sequences submitted to GISAID for the state of Arizona within the last 90 days. Visualization was performed using the python library plotly express and presented in a dashboard using the python library streamlit.

Local directory structure should emulate the format in the visualization folder for this repository.

• The main streamlit script should be in the parent directory while dashboard pages, and data should reside in their respective sub-directories.
• For more information on how to execute the script, visit this streamlit help page.

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Roadmap

• Continued development of analysis and visualization script.